Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

Browett, Sam; McHugo, Gillian P.; Richardson, Ian W.; Magee, David A.; Park, Stephen D. E.; Fahey, Alan G.; Kearney, John F.; Correia, Carolina N.; Randhawa, Imtiaz A. S.; MacHugh, David E.

doi:10.3389/fgene.2018.00051

Cited by 29 publications

(26 citation statements)

References 87 publications

(116 reference statements)

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“…The CSS approach was developed to investigate genomic signatures of selection and has been successful at localizing genes for monogenic and polygenic traits under selection in livestock 24,25,89 . The CSS uses fractional ranks of constituent tests and does not incorporate the statistics with P values, allowing a combination of the evidence of historical selection from different selection tests.…”

Section: Methodsmentioning

confidence: 99%

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

McGivney

Han

Corduff

et al. 2020

Sci Rep

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The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (F iS R 2 = 0.942, P = 2.19 × 10 −13 ; F RoH R 2 = 0.88, P = 1.81 × 10 −10 ) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomicsbased methods will be beneficial to actively monitor the population to address the marked inbreeding trend.The Thoroughbred is among the fastest animals selected by humans for sport, originating from "the commingled blood of Arabs, Turks and Barbs" 1 crossed with local British and Irish mares 2 "but selection and training have together made him a very different animal from his parent-stocks" 1 . The Thoroughbred is now a large (N ~ 500,000) global breed but, in the context of modern horse breeds, it has very low genetic diversity 3,4 due to the limited foundation alleles at the establishment of the stud book and restriction of external gene flow subsequent to the closing of the population 5-7 . In Thoroughbred horse breeding selection of potential champion racehorses is a global multi-billion-dollar business, but there is no systematic industry-mediated genomic selection or genetic population management. We hypothesised that the market-driven emphasis on highly valuable pedigrees and the common practice of inbreeding to successful ancestors in attempts to reinforce...

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Section: Methodsmentioning

confidence: 99%

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

McGivney

Han

Corduff

et al. 2020

Sci Rep

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“…With the advancement of high-throughput genotyping technology, millions of cattle have been genotyped using low, medium or high-density SNP arrays [6,7]. The availability of dense genotype data is a prerequisite to characterize genomic diversity and detect signatures of selection within and between cattle breeds [8][9][10][11][12][13][14]. Moreover, genome-wide association testing between dense array-called genotypes and a broad spectrum of phenotypes revealed thousands of quantitative trait loci (QTL) for complex and monogenic traits [15].…”

Section: Introductionmentioning

confidence: 99%

Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

Bhati

Kadri

Crysnanto

et al. 2019

Preprint

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Background: Local cattle breeds represent an important source of genetic variation because they might carry alleles that enable them to adapt to harsh environments and scarce food conditions. One such local Swiss cattle breed is Original Braunvieh (OB) which is used for beef and milk production in alpine areas. Using whole-genome sequencing data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. Results:We annotated 15.7 million SNPs and 1.5 million Indels including 10,738 and 2,763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10 -3 ) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding (F ROH =0.14) was relatively low in OB cattle. However, genomic inbreeding increased in recent years due to a higher number of long (> 1 Mb) runs of homozygosity in cattle born in more recent generations. Using two complementary approaches, i.e., composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (p < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. Conclusions:We provide a comprehensive overview of genomic variation segregating in Swiss OB cattle. Using whole-genome sequencing data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds.Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to harsh environments. Considering the low population size and increasing rates of genomic inbreeding in the past generations, the implementation and adoption of genomic mating programs seems warranted to maintain genetic diversity in the Swiss OB cattle population.

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“…The CSS approach was developed to investigate genomic signatures of selection and has been successful at localizing genes for monogenic and polygenic traits under selection in livestock [24, 25, 95]. The CSS uses fractional ranks of constituent tests and does not incorporate the statistics with P values, allowing a combination of the evidence of historical selection from different selection tests.…”

Section: Methodsmentioning

confidence: 99%

Genomic inbreeding trends in the global Thoroughbred horse population driven by influential sire lines and selection for exercise trait-related genes

et al. 2019

Preprint

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13The Thoroughbred horse is a highly valued domestic animal population under strong 14 selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of 15 inbreeding in the population that may form the basis for evidence-based discussion amid concerns 16 in the breeding industry over the increasing use of small numbers of popular sire lines, which 17 may accelerate a loss of genetic diversity. In the most comprehensive globally representative 18 sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the 19 major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has 20 been a highly significant decline in global genetic diversity during the last five decades (FIS R 2 = 21 0.942, P = 2.19 × 10 -13 ; FROH R 2 = 0.88, P = 1.81 × 10 -10 ) that has likely been influenced by the use 22 of popular sire lines. Estimates of effective population size in the global and regional populations 23 indicate that there is some level of regional variation that may be exploited to improve global 24 genetic diversity. Inbreeding is often a consequence of selection, which in managed animal 25 populations tends to be driven by preferences for cultural, aesthetic or economically 26 advantageous phenotypes. Using a composite selection signals approach, we show that centuries 27 of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in 28 behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at 29 core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal 30 growth and development, cellular stress and injury, metabolic pathways and neurotransmitters 31 and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our 32 results demonstrate that genomics-based approaches to identify genetic outcrosses will add 33 valuable objectivity to augment traditional methods of stallion selection and that genomics-based 34 methods will be beneficial to actively monitor the population to address the marked inbreeding 35 trend. 36 Author Summary 37In the highly valuable global Thoroughbred horse industry, there is no systematic industry-38 mediated genetic population management. Purposeful inbreeding is common practice and there is an 39 increasing use of popular sires. Inbreeding can lead to population health and fertility decline, but there 40 is little objective genomics-based data for the Thoroughbred to catalyse action and support changes in 41 breeding practices. Here, we describe the most comprehensive genetic analysis in the population among 42 10,000 Thoroughbreds from the major bloodstock regions of the world and reveal a highly significant 43 increase in inbreeding during the last five decades. The main drivers of genetic diversity are the most 44 influential 'breed-shaping' sire lines, Sadler's Wells, Danehill and A.P. Indy. We identified genomic 45 regions subject to positive selection containing genes f...

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Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

Cited by 29 publications

References 87 publications

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

Genomic inbreeding trends in the global Thoroughbred horse population driven by influential sire lines and selection for exercise trait-related genes

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